Raw data: multispecies amplicon sequencing (Loera, Studer, and Kölliker, 2021, Molecular Ecology Resources)

Grasslands cover close to two fifths of Earth's land. They provide
many ecosystem services related to the maintenance of soil integrity, and
the regulation of water, carbon and nitrogen flows. Grasslands constitute
the basis for sustainable roughage production for ruminant feeding.
In Switzerland, grasslands cover more than 70% of the total
agricultural land, which highlights their importance in the domestic food
production chains. Plant genetic diversity (PGD), a component of
biodiversity, influences ecosystem functioning in grasslands. High levels
of grassland PGD are related to resistance against invasive
plants and yield stabilization during environmental stress (e.g., drought
or frost). The PGD of grasses and legumes —the two most
economically relevant plant families found in grasslands, which naturally
grow in a wide climate spectrum— harbors valuable genetic resources for
forage breeding. Nevertheless, most PGD studies of natural or semi-natural
grasslands (i.e., grasslands that are not sown) focus on a single or a few
related species. Traditional PGD monitoring methods (e.g., simple sequence
repeats, or SSRs) are ill-suited for large-scale, multispecies
assessments.  This limits our ability to study the ecological
effects of grassland PGD, its spatiotemporal patterns, and its
significance for grassland management. Looking to provide cost-effective
tools for multispecies PGD monitoring in grasslands, we performed
a sequence capture assay targeting 611 single-copy nuclear loci, followed
by multispecies amplicon sequencing (i.e., amplicon sequencing using
primer pairs that can be used in multiple species) on eleven selected
loci. Our results indicate that multispecies amplicon sequencing
is a cost-effective tool for genetic diversity assessment in grassland
plant species. Furthermore, the sequence capture data provides
the means to extend the number of multispecies amplicons for further
research.